'90 3vze water pump scorched, block scorched
 

I have a 1990 toyota 2W drive 1-ton truck. I removed my water pump from the engine block. After trying to clean the surface of the engine block that meets the water pump, i noticed that the block appears scorched, especially where the water pump rubber O-ring gasket met the engine block. Engine block also appears to have pox marks. Is this a known issue? My new water pump does not use the O-ring rubber type gasket but the paper gasket. How do i get the engine block clearn and smooth enough so that i do not get leaks? Additionally, thermostat cover also looks similar to engine block, looks burned and stained, can not get completely clean. What do I do in this situation?

Its hard to say without seeing it, can you get a few pictures?